VelvetFistIronGlove wrote this in a thread today where i had the near same problem
Some brush entities, like func_door, trigger_multiple, func_door_rotating have an "origin" setting, which is a point in the map. For func_door_rotating, this is the point which the door rotates about, but as far as I know it has no effect with func_door or trigger_multiple. If you turn "View, Show Helpers" on, you can see the origin of the selected entity as a blue ball.

Now if move one of these entities, the origin does not move with it; but if you clone one it does. So cloning and moving these can easily end up with an origin point nowhere near the entity, and sometimes even outside the map.

To fix it, you need to find the entity responsible for the leak (the compile log will tell you what kind of entity it is), and fix up the origin. Make sure "Show Helpers" is on, then select the entities of that type that you worked with recently until one of them shows the origin at the end of the pointfile line. Then the easiest way to fix the origin is to select the entity and choose "Tools, Center Origins".

Since this command will also work on multiple entities and center each of their origins, you can fix up all the entities of one type at once. Go to "Edit, Entity report", choose "Brush entities", and "By class" and select the class type. Then click on the first entity in the list and press Shift+End to select them all; then click "Go To" to select them all. Close the entity report window, and choose "Tools, Center Origins".

I didnt test this out yet, but it makes alot of sense to me and it wont hurt to try.